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887 results for “relaxation”
Phase response analyses support a relaxation oscillator model of locomotor rhythm generation in Caenorhabditis elegans
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Data from: Interplay of trophic relaxation and directional selection shapes eco-evolutionary responses to selective harvest in predator-prey systems
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Mimicry in motion and morphology: do information limitation, trade-offs or compensation relax selection for mimetic accuracy?
<p>Many animals mimic dangerous or undesirable prey as a defence from predators. We would expect predators to reliably and exclusively avoid animals that closely resemble dangerous prey, yet imperfect mimics are common. There have been many hypotheses suggested to explain imperfect mimicry, but comparative tests across multiple mimicry systems are needed to determine which are applicable, and which—if any—represent general principles of imperfect mimicry. We tested four hypotheses on Australian ant mimics and found support for only one of them: the information limitation hypothesis. A predator with incomplete information will be unable to discriminate some poor mimics from their models. We also show that since predators must make decisions while they are learning, they are likely to never sample broadly enough to gain and utilise the full information needed to discriminate poor mimics from their models. We found no evidence that one accurate mimetic trait can compensate for another, or that rapid movement reduces selection pressure for good mimicry. Based on our results, we argue that information limitation is likely to be a general principle behind imperfect mimicry of any complex traits, while interactions between components of mimicry may apply to some mimicry systems but not others.</p>
Insights from empirical analyses and simulations on using multiple fossil calibrations with relaxed clocks to estimate divergence times
<p>Relaxed clock methods account for among-branch-rate-variation when estimating divergence times by inferring different rates for individual branches. In order to infer different rates for individual branches, important assumptions are required. This is because molecular sequence data does not provide direct information about rates, but instead provides direct information about the total number of substitutions along any branch, which is a product of the rate and time for that branch. Often, the assumptions required for estimating rates for individual branches depend heavily on the implementation of multiple fossil calibrations in a single phylogeny. Here, we show that the basis of these assumptions is often critically undermined. First, we highlight that the temporal distribution of the fossil record often violates key assumptions of methods that use multiple fossil calibrations with relaxed clocks. With respect to "node calibration" methods, this conclusion is based on our inference that different fossil calibrations are unlikely to reflect the relative ages of different clades. With respect to the fossilised-birth-death-process, this conclusion is based on our inference that the fossil recovery rate is often highly heterogeneous. We then demonstrate that methods of divergence time estimation that use multiple fossil calibrations are highly sensitive to assumptions about the fossil record and among-branch-rate-variation. Given the problems associated with these assumptions, our results highlight that using multiple fossil calibrations with relaxed clocks often does little to improve the accuracy of divergence time estimates.</p> <p> </p>
Data from: Relaxation of putative plant defenses in a tropical agroecosystem
<p>Evidence of the effects of agriculture on natural systems is widespread, but potential evolutionary responses in non-target species are largely uncharacterized. To explore whether exposure to agrochemicals may influence selective pressures and phenotypic expression in non-agricultural plant populations, we characterized the expression of putative anti-herbivore defense phenotypes in three non-agricultural species found upstream and downstream of irrigated rice fields in Guanacaste Province, Costa Rica. We found that plants downstream of chemically intensive agriculture showed shifts toward reduced expression of putative anti-herbivore defenses relative to upstream counterparts. In two of three tested species, leaf extracts from downstream plants were more palatable to a generalist consumer, suggesting a possible reduction of chemical defenses. In one species with multiple modes of putative defenses, we observed parallel reductions of three metrics of putative biotic and physical defenses. These reductions were concurrent with reduced herbivore damage on downstream plants. Together, these results suggest that agriculture has the potential to alter intraspecific phenotypic expression, ecological interactions, and natural selection in non-target plant populations.</p>
Microscale braid geometry relaxation
<p>Yarn yarn collission of high resolution meshes, derived from graphs.</p>
Pervasive relaxed selection on spermatogenesis genes in gorillas coincident with the evolution of polygyny
<p>Gorillas have a polygynous social system in which the highest-ranking male has almost exclusive access to females and sires most of the offspring in the troop. Such behavior results in a dramatic reduction of sperm competition, which is ultimately associated with numerous traits leading to a low efficacy of gorilla spermatogenesis. However, the molecular basis behind the remarkable erosion of the gorilla male reproductive system remains unknown. Here, we explored the genetic consequences of the polygynous social system in gorillas by testing for altered selection intensity across 13,310 orthologous protein-coding genes from 261 Eutherian mammals. We identified 578 genes with relaxed purifying selection in the gorilla lineage, compared with only 96 that were positively selected. Genes under relaxed purifying selection in gorillas have accumulated numerous deleterious amino acid substitutions; their expression is biased towards male germ cells, and are enriched in functions related to meiosis and sperm biology. We tested the function of gorilla relaxed genes previously not implicated in sperm biology using the Drosophila model system and identified 41 novel spermatogenesis genes required for normal fertility. Furthermore, by exploring exome/genome sequencing data of infertile men with severe spermatogenic impairment, we found that the human orthologs of the gorilla relaxed genes are enriched for loss-of-function variants in infertile men. These data provide compelling evidence that reduced sperm competition in gorillas is associated with relaxed purifying selection on genes related to male reproductive function. The accumulation of deleterious mutations in these genes likely provides the mechanistic basis behind the low efficacy of gorilla spermatogenesis and uncovers new candidate genes for human male infertility.</p>
Relaxed-rate data generated and analysed for Lambert, Valente & Etienne 2023
<p>This repository contains the data for accompanying the PhD research by Lambert et al. (2023), investigating the variation of biodiversity dynamics on islands. The data upload contains two folders. The logs folder contains are plain text logs from running the DAISIE models on the University of Groningen Hábrók High Performance Computing Cluster (HPCC). There is one log per HPCC job. The results folder contains folders for each archipelago included in the study and within each of those folders are model output from the DAISIE R package. Each result is stored as an .rds file. Data was generated and analysed using the relaxedDAISIE and DAISIE R packages. The code for these packages is version controlled on GitHub and is freely available in open-source repositories. See the Related Identifiers section for links to relevant archived versions of both these packages.</p>
Experimental evolution of Dictyostelium discoideum cheating under relaxed selection
<p>Many microbes interact with one another, but the difficulty of directly observing these interactions in nature makes interpreting their adaptive value complicated. The social amoeba <em>Dictyostelium discoideum </em>forms aggregates<em> </em>wherein some cells are sacrificed for the benefit of others. Within chimeric aggregates containing multiple unrelated lineages, cheaters can gain an advantage by undercontributing, but the extent to which wild <em>D. discoideum </em>has adapted to cheat is not fully clear. In this study, we experimentally evolved <em>D. discoideum </em>in an environment where there were no selective pressures to cheat or resist cheating in chimeras. <em>D. discoideum </em>lines grown in this environment evolved reduced competitiveness within chimeric aggregates and reduced ability to migrate during the slug stage. By contrast, we did not observe a reduction in cell number, a trait for which selection was not relaxed. The observed loss of traits that our laboratory conditions had made irrelevant suggests that these traits were adaptations driven and maintained by selective pressures <em>D. discoideum </em>faces in its natural environment. Our results suggest that <em>D. discoideum</em> faces social conflict in nature, and illustrate a general approach that could be applied to searching for social or non-social adaptations in other microbes.</p>
KupferDigital mechanical testing datasets: Stress relaxation and low-cycle fatigue (LCF) tests
<p><span>The Kupfer<em>Digital</em> project deals with the development of a data ecosystem for digital materials research on the basis of ontology-based digital representations of copper and copper alloys. This document provides exemplary mechanical testing datasets for training the developed Kupfer<em>Digital</em> infrastructures. Different types of cast copper alloys were provided for this research and their mechanical testing (stress relaxation and low-cycle fatigue) was performed in the accredited materials testing laboratory, while the test results were reported according to the DIN/ISO standards and attached with the maximum possible metadata about the sample history, equipment, and calibration. The attached content file consisted of the obtained primary raw testing data as well as the secondary datasets of these tests containing the detailed metadata of mechanical testing methods. Such test data files are processed by the Kupfer<em>Digital</em> digital tools to be converted to standardized machine-readable data files.</span></p>
Data for Spaulding-Astudillo and Mitchell (2024a), "A simple model for the emergence of relaxation-oscillator convection"
<p>Data for Spaulding-Astudillo and Mitchell (2024a), "A simple model for the emergence of relaxation-oscillator convection"</p> <p>The main directories have a common nomenclature: e.g., minimal_1p1S_FSC_335K_N7200, where 1p1S indicates a solar constant 1.1 times the present day (1360), FSC indicates that it is a full-sky radiation run, 335 K is the surface temperature (fixed), and N7200 refers to the relaxation timescale of 7200 seconds for CAPE in the quasi-equilibrium closure to the convection scheme. </p> <p>In every directory, each .nc file contains 5 years of model output. There are 5 types of .nc files, which correspond to different output streams of ECHAM6. The main output stream is ..._echam.nc, which has daily-averaged output.</p> <p>The tendencies for gross deposition (gdep_ls) and gross condensation (gcnd_ls; both with units of kg/m2/s) from the large-scale scheme are in ..._g1am.nc. This is the mean-value stream, which records daily-averaged values. </p> <p>The tendencies for gross condensation in convective updrafts are stored in the variable "ddf13" in ..._debugs.nc (units of kg/m2/s). This is another output stream, which records hourly values usually for debugging purposes. The total pressure as a function of height (units of Pa) is stored in the variable "ddf8". Also, the implied surface heat source/sink in the surface energy budget that keeps the surface temperature fixed in time is tracked in the variable "zdf8" (units of W/m2). </p> <p>The experimental range of surface temperatures is 290-360 K, which remain fixed as a function of time in the simulations through the use of an artificial heat sink. The simulations are from the ECHAM6 climate model, which we ran in single-column mode. </p>
Grid-Free Evaluation of Phonon-Limited Relaxation Times and Electrical Transport Properties
<p>Data, source codes and figures for the manuscript:</p> <p>"Grid-Free Evaluation of Phonon-Limited Relaxation Times and Electrical Transport Properties"</p>
Relaxed selection and the evolution of Chasmogamous flower of Impatiens capensis
<p><span><span><span><span><span><span><span><span><span><span><span>We exploited ecotypic variation in <i>Impatiens capensis</i> to test the hypothesis that mutation accumulation accompanying relaxed selection on the chasmogamous (CH) flower leads to more variable flower shapes and smaller flowers. Sun ecotype populations of this species occur along sunny riverbanks and marshes and produce both CH and cleistogamous (CL) flowers, while shade ecotype populations occur in shady forest floors and produce only CL flowers. In the shade ecotype, it is assumed that selection on the CH flower has been relaxed. Seedlings from population samples of the two ecotypes exhibited different first internode growth responses to low ratio of red:far-red light characteristic of ecotypic differentiation to either sunny or shady conditions, helping to verify historical illumination conditions in the populations. We examined the CH floral mutation accumulation hypothesis by comparing the shape and size of the modified CH flower sepal under greenhouse conditions that triggered CH flowering in plants of both ecotypes. Contrary to our predictions, geometric morphometric analysis of sepal shape variation levels indicated little difference between the shade and sun ecotypes. We suggest that mutations that influence CH flower shape may have pleiotropic effects on structures or processes that remain under selection even when the CH flowers are not produced. On the other hand, sepal size was significantly smaller in the shade ecotype populations. In the case of CH sepal size, the mutational effects appear to be directional, towards the production of smaller sepals, and likely would be deleterious if shade ecotype plants encountered sunnier conditions where CH flowers could be produced. </span></span></span></span></span></span></span></span></span></span></span></p>
Dipolar Relaxation of Water Protons in the Vicinity of a Collagen-Like Peptide: Input Files for Simulation
<p>Input files to run the simulations in the paper</p> <p>Journal: The Journal of Physical Chemistry B<br> Title: Dipolar relaxation of water protons in the vicinity of a collagen-like peptide<br> Authors: Jouni Karjalainen, Henning Henschel, Mikko J. Nissi, Miika T. Nieminen, Matti Hanni<br> DOI: 10.1021/acs.jpcb.2c00052</p>
Data-driven capacity estimation of commercial lithium-ion batteries from voltage relaxation
<p>Here are the datasets for the publication named "Data-driven capacity estimation of commercial lithium-ion batteries from voltage relaxation" published in Nature Communications. Experimental cycling data for three commercial 18650 type batteries (Dataset_1:NCA battery, Dataset_2:NCM battery, and Dataset_3:NCM+NCA_battery) are given, where each csv file corresponds to one cell cycling data. The cells are named as CY<em>X-Y_Z</em>-#<em>N</em> according to their cycling conditions. <em>X</em> means the temperature, <em>Y_Z</em> represents the charge_discharge current rate, #<em>N</em> is the cell tag. Each csv file has 9 columns, including cycle time ('time/s'), controlled voltage and current ('control/V/mA'), battery voltage ('Ecell/V'), applied current ('<I>/mA'), charge or discharge electricity ('Q discharge/mA.h' and 'Q discharge/mA.h'), controlled voltage or current ('control/V', 'control/mA' and ), and cycle number ('cycle number'). In the impedance data, one representative cell from each cycling condition is chosen for the discussion in the main text. More detailed descriptions can be found in the zip file.</p>
Monks relax sibling competition over parental resources in Tibetan populations
<p class="MsoNormal"><span>Why parents in some societies induce some of their sons to become religious celibates is an evolutionary puzzle. Some have speculated that this might be associated with brother competition for family resources. However, the behavioral ecology of monks and the possible links with competition between brothers remains unexplored. Here, we use demographic data from Amdo Tibetan agropastoralists in western China to evaluate what factors determine the probability of becoming a monk and explore the possible association between wealth and having a monk brother. We found that boys with at least one older brother are more likely to be induced by their parents to become celibate monks. Patrilocal heads of household, who inherit parental property, are more likely to be first-born sons, whereas men who marry uxorilocally, that is they move to their wife's household, are generally second or later born sons. Moreover, we find that men with at least one monk brother are wealthier than men who only have non-celibate brothers. Together, these results suggest that sending a son to the monastery is way for parents to decrease competition between brothers over family resources. Harsh and resource-limited environments, like the one we consider, can lead to the emergence of communal households, including polyandrous families, which used to be common in Tibetan areas. Directing one son to become a religious celibate offers a potentially effective solution to brother competition in our population.</span></p>
Mean sea-level pressure and related indices from control and tropical relaxation winter seasonal hindcasts using the Met Office GloSea5 system.
<p>© Crown Copyright, Met Office</p> <p>The accompanying data is made available under the terms of the Non-Commercial Government Licence (http://www.nationalarchives.gov.uk/doc/non-commercial-government-licence/version/2/).</p> <p>These data are the results of ensemble modelling simulations using the Met Office GloSea5 numerical seasonal prediction system. Files in (zipped) netcdf format contain winter seasonal-mean mean sea-level pressure (MSLP) fields for each member of specified ensemble and hindcast winter (December-February from 1993-94 to 2015-16). The files are named according to the specification of relaxation towards observational reanalysis in each. HCAST has no relaxation, ALL has tropical (approximately 22.5S to 22.5N) relaxation at all atmospheric heights, TROP is similar to ALL but with relaxation limited to below 18km and STRAT is similar to ALL but with relaxation limited to above 18km. The relaxation is designed to constrain the atmospheric state to be close to that which was observed within the domain over which it is applied. Details of the technique can be found in Maidens et al., 2021* and references therein.</p> <p>An additional text file is provided to give summary statistics of key MSLP-based winter indices.</p> <p> </p> <p>* Maidens, A., Knight, J. R., & Scaife, A. A. (2021). Tropical and stratospheric influences on winter atmospheric circulation patterns in the North Atlantic sector. Environmental Research Letters, 16, 024035. https://doi.org/10.1088/1748-9326/abd8aa</p> <p> </p>
Data and analysis for the paper "Nonlocal measurement of quasiparticle charge and energy relaxation in proximitized semiconductor nanowires using quantum dots"
<p>This repository contains the raw data and analysis code used to generate the figures in the manuscript <em>Nonlocal measurement of quasiparticle charge and energy relaxation in proximitized semiconductor nanowires using quantum dots</em>. </p> <p><a href="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.106.064503">Link to publication</a></p> <p><a href="https://arxiv.org/abs/2110.05373">Link to arXiv</a></p>
New methods for robust continuous wave T1ρ relaxation preparation
<p>This dataset contains all the raw source data, MATLAB analysis functions and files, and article figures that comprise the study:</p> <p><br> New methods for robust continuous wave T1ρ relaxation preparation</p> <p>NMR in Biomedicine, 2022. </p> <p>Pala S(1), Hänninen NE(1,2), Nykänen O(1), Liimatainen T(2,3), Nissi MJ(1,2)*</p> <p>(1) Department of Applied Physics, University of Eastern Finland, POB 1627, FI-70211 Kuopio, Finland<br> (2) Research Unit of Medical Imaging, Physics and Technology, University of Oulu, POB 5000, FI-90014 Oulu, Finland<br> (3) Department of Radiology, Oulu University Hospital, Oulu, Finland</p> <p>*Corresponding author:<br> Mikko J. Nissi<br> Department of Applied Physics,<br> University of Eastern Finland<br> POB 1627<br> FI-70211, Kuopio, Finland<br> mikko.nissi@uef.fi<br> +358-50-5955517</p> <p><br> Keywords: contrast, T1ρ relaxation, field inhomogeneity, rotating frame of reference, bloch simulation. </p> <p>Included folders and files are:<br> - article_figures: all figures published in the manuscript and in the supplementary document (.svg format)<br> - experimental Data: .fid files of the MRI measurements ordered, the script for comparison of methods and supporting files (ROIs and masks), and corresponding mono-exponential fitted T1 rho maps.<br> - macro_files: VnmrJ macro files for setting up the measurements using all the pulse schemes discussed in the manuscript and supplementary documents.<br> - RF_Pulse_sequences: VnmrJ RF waveforms used in the study, generated using the included Matlab functions<br> - matlab_functions: Matlab functions used for creating the RF waveforms (T1rho pulse schemes) and for data analysis with subfolders and files:<br> - aedes_plugins: plugins for aedes (http://aedes.uef.fi) and scripts to read all raw data files for calculation of relaxation time maps - miscellaneous_functions: Pulse generation functions and other functions (Pulse generation, sequence reading and display, and pulse simulation scripts) and also scripts for RMS calculation.<br> - PulseTrain_Generator.m: GUI tool for using the various included scripts for creating the RF waveforms used in the study<br> - README.txt: this file describing the contents of the dataset</p> <p><br> See more info in separate readme files included in sub-folders.<br> </p>
Two notorious nodes: A critical examination of relaxed molecular clock age estimates of the bilaterian animals and placental mammals
<p><span>The popularity of relaxed clock Bayesian inference of clade origin timings has generated several recent publications with focal results considerably older than the fossils of the clades in question. Here we critically examine two such clades: the animals (with focus on the bilaterians); and the mammals (with focus on the placentals). Each example displays a set of characteristic pathologies which, although much commented on, are rarely corrected for. We conclude that in neither case does the molecular clock analysis provide any evidence for an origin of the clade deeper than what is suggested by the fossil record. In addition, both these clades have other features (including, in the case of the placental mammals, proximity to a large mass extinction) that allow us to generate precise expectations of the timings of their origins. Thus, in these instances the fossil record can provide a powerful test of molecular clock methodology, and why it goes astray; and we have every reason to think these problems are general. </span></p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.